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If one has a sequence clustering one can collect structure properties to make structural predictions or vice versa.
This allowed us to make structural predictions as to differences in LOS seen between commensal and pathogenic strains.
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Because an lncRNA could fold into many different structures, making structural prediction difficult, we examined how the insertion of TEs modified the sequences and structures of the ANRIL exons.
JM performed the structural predictions, made Figures 3 and 4. AL directed the research and wrote the manuscript.
The secondary structure of the expressed lincRNAs was inferred by intersecting their chromosomal positions with the positions of the RNAz structural predictions made across the entire mouse genome, as previously described in the NRED database (Washietl et al. 2005; Mercer et al. 2008; Dinger et al. 2009).
Structural predictions were made and validated.
Returned sequences were added to the alignments and structural predictions were made using RNAalifold as well as the program TurboFold [ 118] followed by manual model refinement.
Secondary structural predictions were initially made using HHpred program and generally predicted two anti-parallel helices per PPR [ 47].
The effects of the Y254V mutation on the translocation step are intriguing, since structural predictions can be made that the mutation disrupts the stacking interaction between Y254 and Y390 in the post-translocation state binary complex and disrupts the stacking interaction between Y254 and the sugar moiety of the primer terminal residue in the pre-translocation state binary complex.
This is often used to make probabilistic structural fracture predictions for combinations of crack length and applied load.
The simplicity and generality of our setting allows us to make predictions for structural parameters of the grid system in different dimensions.
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